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Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
Authors:
- Mateusz Chwastyk,
- Ewa A. Panek,
- Jan Malinowski,
- Mariusz Jaskólski,
- Marek Cieplak
Abstract
We performed a PDB-wide survey of proteins to assess their cavity content, using the SPACEBALL algorithm to calculate the cavity volumes. In addition, we determined the hydropathy character of the cavities. We demonstrate that the cavities of most proteins are hydrophilic, but smaller proteins tend to have cavities with hydrophobic walls. We propose criteria for distinguishing between cavities and pockets, and single out proteins with the largest cavities.
- Record ID
- UAM6360a2d10fb04b1da38d7979d1974900
- Author
- Journal series
- Frontiers in Molecular Biosciences, ISSN , e-ISSN 2296-889X
- Issue year
- 2020
- Vol
- 7
- Pages
- 1-19
- Article number
- 591381
- Keywords in English
- proteins, cavity volume calculation, plant pathogenesis-related proteins, hydrophobicity, signaling proteins, transport proteins
- DOI
- DOI:10.3389/fmolb.2020.591381 Opening in a new tab
- URL
- https://www.frontiersin.org/articles/10.3389/fmolb.2020.591381/full Opening in a new tab
- Language
- (en) English
- Score (nominal)
- 140
- Score source
- journalList
- Score
- = 140.0, 20-05-2022, ArticleFromJournal
- Publication indicators
- = 2; = 0
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- Uniform Resource Identifier
- https://researchportal.amu.edu.pl/info/article/UAM6360a2d10fb04b1da38d7979d1974900/
- URN
urn:amu-prod:UAM6360a2d10fb04b1da38d7979d1974900
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or PerishOpening in a new tab system.